Land-use intensity influences European tetrapod food webs.

Land use intensification favours particular trophic groups which can induce architectural changes in food webs. These changes can impact ecosystem functions, services, stability and resilience. However, the imprint of land management intensity on food-web architecture has rarely been characterized across large spatial extent and various land uses. We investigated the influence of land management intensity on six facets of food-web architecture, namely apex and basal species proportions, connectance, omnivory, trophic chain lengths and compartmentalization, for 67,051 European terrestrial vertebrate communities. We also assessed the dependency of this influence of intensification on land use and climate. In addition to more commonly considered climatic factors, the architecture of food webs was notably influenced by land use and management intensity. Intensification tended to strongly lower the proportion of apex predators consistently across contexts. In general, intensification also tended to lower proportions of basal species, favoured mesopredators, decreased food webs compartmentalization whereas it increased their connectance. However, the response of food webs to intensification was different for some contexts. Intensification sharply decreased connectance in Mediterranean and Alpine settlements, and it increased basal tetrapod proportions and compartmentalization in Mediterranean forest and Atlantic croplands. Besides, intensive urbanization especially favoured longer trophic chains and lower omnivory. By favouring mesopredators in most contexts, intensification could undermine basal tetrapods, the cascading effects of which need to be assessed. Our results support the importance of protecting top predators where possible and raise questions about the long-term stability of food webs in the face of human-induced pressures.

Vulnerability of terrestrial vertebrate food webs to anthropogenic threats in Europe.

Vertebrate species worldwide are currently facing significant declines in many populations. Although we have gained substantial knowledge about the direct threats that affect individual species, these threats only represent a fraction of the broader vertebrate threat profile, which is also shaped by species interactions. For example, threats faced by prey species can jeopardize the survival of their predators due to food resource scarcity. Yet, indirect threats arising from species interactions have received limited investigation thus far. In this study, we investigate the indirect consequences of anthropogenic threats on biodiversity in the context of European vertebrate food webs. We integrated data on trophic interactions among over 800 terrestrial vertebrates, along with their associated human-induced threats. We quantified and mapped the vulnerability of various components of the food web, including species, interactions, and trophic groups to six major threats: pollution, agricultural intensification, climate change, direct exploitation, urbanization, and invasive alien species and diseases. Direct exploitation and agricultural intensification were two major threats for terrestrial vertebrate food webs: affecting 34% and 31% of species, respectively, they threaten 85% and 69% of interactions in Europe. By integrating network ecology with threat impact assessments, our study contributes to a better understanding of the magnitude of anthropogenic impacts on biodiversity.

Identifying outcomes reported in exercise interventions in oesophagogastric cancer survivors: a systematic review.

BACKGROUND: Research investigating exercise interventions in oesophagogastric cancer survivors is sparse, and the outcomes are varied. The aim of this systematic review is to identify the domains and outcomes reported in exercise interventions in oesophagogastric cancer survivors to be included in a Delphi study, with a view to informing the development of a core outcome set (COS). METHODS: EMBASE, PubMed, CINHAL, Cochrane Library, SCOPUS, and PEDro were searched up to March 2020 using a predefined search strategy. The outcomes identified during data extraction were categorised using the core areas outlined in the OMERACT Filter 2.0. RESULTS: Fourteen domains and 63 outcomes were identified. The most frequently reported outcomes were in the domains of quality of life using the EORTC-QLQ-C30 questionnaire and the relevant disease-specific modules (100%), exercise capacity/fitness/physical function (100%), anthropometrics (83.33%), physical activity (66.67%), and biomarker analysis (50%). CONCLUSION: This systematic review quantifies and describes the domains and outcomes examined in exercise interventions in oesophagogastric cancer survivors. Some inconsistency exists within the domains and outcomes used, and little attention was given to nutritional or economic endpoints. In order to develop a COS, a Delphi consensus process with key stakeholders is needed to identify the relevant domains and outcomes for inclusion.

Coordinate expression loss of GKN1 and GKN2 in gastric cancer via impairment of a glucocorticoid-responsive enhancer.

Gastrokines (GKNs) are anti-inflammatory proteins secreted by gastric epithelial (surface mucous and pit) cells, with their aberrant loss of expression causally linked to premalignant inflammation and gastric cancer (GC). Transcriptional mechanisms accounting for GKN expression loss have not been elucidated. Using human clinical cohorts, mouse transgenics, bioinformatics, and transfection/reporter assays, we report a novel mechanism of GKN gene transcriptional regulation and its impairment in GC. GKN1/GKN2 loss is highly coordinated, with both genes showing parallel downregulation during human and mouse GC development, suggesting joint transcriptional control. In BAC transgenic studies, we defined a 152-kb genomic region surrounding the human GKN1/GKN2 genes sufficient to direct their tissue- and lineage-restricted expression. A screen of the 152-kb region for candidate regulatory elements identified a DNase I hypersensitive site (CR2) located 4 kb upstream of the GKN1 gene. CR2 showed overlapping enrichment of enhancer-related histone marks (H3K27Ac), a consensus binding site (GRE) for the glucocorticoid receptor (GR), strong GR occupancy in ChIP-seq data sets and, critically, exhibited dexamethasone-sensitive enhancer activity in reporter assays. Strikingly, GR showed progressive expression loss, paralleling that of GKN1/2, in human and mouse GC, suggesting desensitized glucocorticoid signaling as a mechanism underlying GKN loss. Finally, mouse adrenalectomy studies revealed a critical role for endogenous glucocorticoids in sustaining correct expression (and anti-inflammatory restraint) of GKNs in vivo. Together, these data link the coordinate expression of GKNs to a glucocorticoid-responsive and likely shared transcriptional enhancer mechanism, with its compromised activation contributing to dual GKN loss during GC progression.NEW & NOTEWORTHY Gastrokine 2 (GKN2) is an anti-inflammatory protein produced by the gastric epithelium. GKN2 expression is progressively lost during gastric cancer (GC), which is believed to play a casual role in GC development. Here, we use bacterial artificial chromosome transgenic studies to identify a glucocorticoid-responsive enhancer element that likely governs expression of GKN1/GKN2, which, via parallel expression loss of the anti-inflammatory glucocorticoid receptor, reveals a novel mechanism to explain the loss of GKN2 during GC pathogenesis.

Diversity indices for ecological networks: a unifying framework using Hill numbers.

Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to understand and predict ecosystem trajectories. However, it requires having an appropriate framework to measure network diversity locally, regionally and between samples (α-, γ- and ß-diversity). Here, we propose a unifying framework that builds on Hill numbers and accounts both for the probabilistic nature of biotic interactions and the abundances of species or groups. We emphasise the importance of analysing network diversity across different species aggregation levels (e.g. from species to trophic groups) to get a better understanding of network structure. We illustrate our framework with a simulation experiment and an empirical analysis using a global food-web database. We discuss further usages of the framework and show how it responds to recent calls on comparing ecological networks and analysing their variation across environmental gradients and time.

Overexpression of IL-11 promotes premalignant gastric epithelial hyperplasia in isolation from germline gp130-JAK-STAT driver mutations.

Expression of the cytokine IL-11 is elevated in human Helicobacter pylori infection and progressively increases with worsening gastric pathology. Additionally, IL-11 is required for tumor development in STAT3-dependent murine models of gastric cancer (GC) and, when administered acutely, causes resolving atrophic gastritis. However, it is unclear whether locally elevated IL-11 ligand expression can, in isolation from oncogenic gp130-JAK-STAT pathway mutations, initiate GC pathogenesis. Here we developed a transgenic mouse model of stomach-specific (keratin 19 promoter) IL-11 ligand overexpression. Keratin 19 promoter-IL-11 transgenic ( K19-IL11Tg) mice showed specific IL-11 overexpression in gastric corpus and antrum but not elsewhere in the gastrointestinal tract or in other tissues. K19-IL11Tg mice developed spontaneous premalignant disease of the gastric epithelium, progressing from atrophic gastritis to TFF2-positive metaplasia and severe epithelial hyperplasia, including adenoma-like lesions in a subset of older (1 yr old) animals. Although locally advanced, the hyperplastic lesions remained noninvasive. H. pylori infection in K19-IL11Tg mice accelerated some aspects of the premalignant phenotype. Finally, K19-IL11Tg mice had splenomegaly in association with elevated serum IL-11, with spleens showing an expanded myeloid compartment. Our results provide direct in vivo functional evidence that stomach-specific overexpression of IL-11, in isolation from germline gp130-JAK-STAT3 genetic drivers, is sufficient for premalignant progression. These findings have important functional implications for human GC, in which frequent IL-11 overexpression occurs in the reported absence of somatic mutations in gp130 signaling components. NEW & NOTEWORTHY We provide direct in vivo functional evidence that stomach-specific overexpression of the cytokine IL-11, in isolation from gp130-JAK-STAT3 pathway mutations, can trigger spontaneous atrophic gastritis progressing to locally advanced epithelial hyperplasia (but not dysplasia or carcinoma), which does not require, but may be accelerated by, concomitant Helicobacter pylori infection.

Intraoperative interventions for preventing surgical site infection: an overview of Cochrane Reviews.

BACKGROUND: Surgical site infection (SSI) rates vary from 1% to 5% in the month following surgery. Due to the large number of surgical procedures conducted annually, the costs of these SSIs can be considerable in financial and social terms. Many interventions are used with the aim of reducing the risk of SSI in people undergoing surgery. These interventions can be broadly delivered at three stages: preoperatively, intraoperatively and postoperatively. The intraoperative interventions are largely focused on decontamination of skin using soap and antiseptics; the use of barriers to prevent movement of micro-organisms into incisions; and optimising the patient's own bodily functions to promote best recovery. Both decontamination and barrier methods can be aimed at people undergoing surgery and operating staff. Other interventions focused on SSI prevention may be aimed at the surgical environment and include methods of theatre cleansing and approaches to managing theatre traffic. OBJECTIVES: To present an overview of Cochrane Reviews of the effectiveness and safety of interventions, delivered during the intraoperative period, aimed at preventing SSIs in all populations undergoing surgery in an operating theatre. METHODS: Published Cochrane systematic reviews reporting the effectiveness of interventions delivered during the intraoperative period in terms of SSI prevention were eligible for inclusion in this overview. We also identified Cochrane protocols and title registrations for future inclusion into the overview. We searched the Cochrane Library on 01 July 2017. Two review authors independently screened search results and undertook data extraction and 'Risk of bias' and certainty assessment. We used the ROBIS (risk of bias in systematic reviews) tool to assess the quality of included reviews, and we used GRADE methods to assess the certainty of the evidence for each outcome. We summarised the characteristics of included reviews in the text and in additional tables. MAIN RESULTS: We included 32 Cochrane Reviews in this overview: we judged 30 reviews as being at low risk of bias and two at unclear risk of bias. Thirteen reviews had not been updated in the past three years. Two reviews had no relevant data to extract. We extracted data from 30 reviews with 349 included trials, totaling 73,053 participants. Interventions assessed included gloving, use of disposable face masks, patient oxygenation protocols, use of skin antiseptics for hand washing and patient skin preparation, vaginal preparation, microbial sealants, methods of surgical incision, antibiotic prophylaxis and methods of skin closure. Overall, the GRADE certainty of evidence for outcomes was low or very low. Of the 77 comparisons providing evidence for the outcome of SSI, seven provided high- or moderate-certainty evidence, 39 provided low-certainty evidence and 31 very low-certainty evidence. Of the nine comparisons that provided evidence for the outcome of mortality, five provided low-certainty evidence and four very low-certainty evidence.There is high- or moderate-certainty evidence for the following outcomes for these intraoperative interventions. (1) Prophylactic intravenous antibiotics administered before caesarean incision reduce SSI risk compared with administration after cord clamping (10 trials, 5041 participants; risk ratio (RR) 0.59, 95% confidence interval (CI) 0.44 to 0.81; high-certainty evidence - assessed by review authors). (2) Preoperative antibiotics reduce SSI risk compared with placebo after breast cancer surgery (6 trials, 1708 participants; RR 0.74, 95% CI 0.56 to 0.98; high-certainty evidence - assessed by overview authors). (3) Antibiotic prophylaxis probably reduce SSI risk in caesarean sections compared with no antibiotics (82 relevant trials, 14,407 participants; RR 0.40, 95% CI 0.35 to 0.46; moderate-certainty evidence; downgraded once for risk of bias - assessed by review authors). (4) Antibiotic prophylaxis probably reduces SSI risk for hernia repair compared with placebo or no treatment (17 trials, 7843 participants; RR 0.67, 95% CI 0.54 to 0.84; moderate-certainty evidence; downgraded once for risk of bias - assessed by overview authors); (5) There is currently no clear difference in the risk of SSI between iodine-impregnated adhesive drapes compared with no adhesive drapes (2 trials, 1113 participants; RR 1.03, 95% CI 0.66 to 1.60; moderate-certainty evidence; downgraded once for imprecision - assessed by review authors); (6) There is currently no clear difference in SSI risk between short-term compared with long-term duration antibiotics in colorectal surgery (7 trials; 1484 participants; RR 1.05 95% CI 0.78 to 1.40; moderate-certainty evidence; downgraded once for imprecision - assessed by overview authors). There was only one comparison showing negative effects associated with the intervention: adhesive drapes increase the risk of SSI compared with no drapes (5 trials; 3082 participants; RR 1.23, 95% CI 1.02 to 1.48; high-certainty evidence - rated by review authors). AUTHORS' CONCLUSIONS: This overview provides the most up-to-date evidence on use of intraoperative treatments for the prevention of SSIs from all currently published Cochrane Reviews. There is evidence that some interventions are useful in reducing SSI risk for people undergoing surgery, such as antibiotic prophylaxis for caesarean section and hernia repair, and also the timing of prophylactic intravenous antibiotics administered before caesarean incision. Also, there is evidence that adhesive drapes increase SSI risk. Evidence for the many other treatment choices is largely of low or very low certainty and no quality-of-life or cost-effectiveness data were reported. Future trials should elucidate the relative effects of some treatments. These studies should focus on increasing participant numbers, using robust methodology and being of sufficient duration to adequately assess SSI. Assessment of other outcomes such as mortality might also be investigated as part of non-experimental prospective follow-up of people with SSI of different severity, so the risk of death for different subgroups can be better understood.

Development and performance evaluation of a recombinase polymerase amplification assay for the rapid detection of group B streptococcus.

BACKGROUND: Despite the implementation of prevention guidelines, group B Streptococcal (GBS) infection remains a leading cause of sepsis, pneumonia, and meningitis, resulting in significant neonatal morbidity and mortality. Preventive approaches that identify women at risk of transmitting GBS have reduced the incidence of neonatal GBS disease, and dramatically decreased the associated mortality rates. However, there is an on-going requirement for a near-patient diagnostic test for GBS that can be carried out at the time of delivery, ideally in the labour ward setting, particularly for women of unknown GBS colonisation status at the time of delivery. METHODS: In this study, a Recombinase Polymerase Amplification (RPA) assay was developed and performance evaluated for the detection of group B Streptococcus in vaginal swabs. The assay uses the cAMP factor (cfb) gene of GBS as the target gene. The analytical performance of the assay was evaluated by testing a panel of GBS reference strains and clinical isolates, and non-GBS organisms. The limit of detection was determined and the clinical performance was evaluated by testing 124 vaginal swabs from women with both GBS positive and negative status. RESULTS: Based on specificity testing carried out the assay was shown to be specific for the target of interest. The limit of detection of the assay was shown to be between six and 12 genome copies and was comparable to that of a real-time PCR assay, both achieving a limit of detection below 12.5 genome copies. The performance of both assays when applied to clinical samples was identical. CONCLUSION: A specific, sensitive RPA assay for GBS was developed. The performance of the assay for testing of clinical samples is within the acceptable range.

Linking biodiversity, ecosystem function, and Nature's contributions to people: a macroecological energy flux perspective.

At macroecological scales, the provision of Nature's contributions to people (NCP) is mostly estimated with biophysical information, ignoring the ecological processes underlying them. This hinders our ability to properly quantify the impact of declining biodiversity and the provision of NCP. Here, we propose a framework that combines local-scale food web energy flux approaches and large-scale biodiversity models to evaluate ecosystem functions and flux-related NCP at extensive spatiotemporal scales. Importantly, this approach has the potential to upscale ecosystem functions, assess the vulnerability of flux-related NCP to the climate crisis, and support the development of multiscale mitigation policies.

An assessment of the state of conservation planning in Europe.

Expanding and managing current habitat and species protection measures is at the heart of the European biodiversity strategy. A structured approach is needed to gain insights into such issues is systematic conservation planning, which uses techniques from decision theory to identify places and actions that contribute most effectively to policy objectives given a set of constraints. Yet culturally and historically determined European landscapes make the implementation of any conservation plans challenging, requiring an analysis of synergies and trade-offs before implementation. In this work, we review the scientific literature for evidence of previous conservation planning approaches, highlighting recent advances and success stories. We find that the conceptual characteristics of European conservation planning studies likely reduced their potential in contributing to better-informed decisions. We outline pathways towards improving the uptake of decision theory and multi-criteria conservation planning at various scales, particularly highlighting the need for (a) open data and intuitive tools, (b) the integration of biodiversity-focused conservation planning with multiple objectives, (c) accounting of dynamic ecological processes and functions, and (d) better facilitation of entry-points and co-design practices of conservation planning scenarios with stakeholders. By adopting and improving these practices, European conservation planning might become more actionable and adaptable towards implementable policy outcomes. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Evaluation of a family liaison officer role introduced during the COVID-19 pandemic: A mixed methods study.

RATIONALE: The restrictions to hospital visiting for carers and relatives during the pandemic were unprecedented. To ensure patients could stay in touch with their relatives and carers new liaison roles were introduced. AIMS AND OBJECTIVES: The aim of this study is to report on the evaluation of a Family Liaison Officer (FLO) role to understand the rationale for introducing the role along with the challenges and benefits of its implementation. METHODS: A concurrent mixed methods design was used, triangulating both semi structured interviews and online surveys. Data were collected during 2021 from postholders, patients/relatives and key stakeholders. RESULTS: The family liaison officer role occupies a key brokering role between clinical teams and patients/relatives. All participants agreed the importance of the role particularly in relation to communication. Postholders noted issues around clarity of scope of practice. Patients reported the social benefits of the FLOs particularly in relation to technology. There was also key learning in terms of induction, training and line management of this nonprofessional role. CONCLUSION: There is limited research that evaluates emerging nonprofessional roles that connect clinical teams and patients/relatives. This evaluation study although limited to one organisation provides important insights to the strategic and operational learning to introducing a family liaison officer role during the COVID-19 pandemic.

Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.

IMPORTANCE: The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.

Recruitment rates and strategies in exercise trials in cancer survivorship: a systematic review.

PURPOSE: Despite clear evidence-based supporting a benefit to exercise on physical and psychological metrics in patients with cancer, recruitment to exercise trials amongst cancer survivors is suboptimal. We explore current recruitment rates, strategies, and common barriers to participation in exercise oncology trials in cancer survivorship. METHODS: A systematic review was conducted using a pre-defined search strategy in EMBASE, CINAHL, Medline, Cochrane Library, and Web of Science. The search was performed up to 28/02/2022. Screening of titles and abstracts, full-text review, and data extraction was completed in duplicate. RESULTS: Of the 3204 identified studies, 87 papers corresponding to 86 trials were included. Recruitment rates were highly variable with a median rate of 38% (range 0.52-100%). Trials recruiting prostate cancer patients only had the highest median recruitment rate (45.9%) vs trials recruiting colorectal cancer patients only which had the lowest (31.25%). Active recruitment strategies such as direct recruitment via a healthcare professional were associated with higher recruitment rates (rho = 0.201, p = 0.064). Common reasons for non-participation included lack of interest (46.51%, n (number of studies) = 40); distance and transport (45.3%, n = 39); and failure to contact (44.2%, n = 38). CONCLUSIONS: Recruitment of cancer survivors to exercise interventions is suboptimal with barriers being predominantly patient-oriented. This paper provides the benchmark for current recruitment rates to exercise oncology trials, providing data for trialists planning future trial design and implementation, optimise future recruitment strategies, and evaluate their own recruitment success against current practice. IMPLICATIONS FOR CANCER SURVIVORS: Enhanced recruitment to cancer survivorship exercise trials is necessary in facilitating the publication of definitive exercise guidelines, generalisable to varying cancer cohorts. PROSPERO REGISTRATION NUMBER: CRD42020185968.

Dissimilarity of vertebrate trophic interactions reveals spatial uniqueness but functional redundancy across Europe.

Identifying areas that contain species assemblages not found elsewhere in a region is central to conservation planning.1,2 Species assemblages contain networks of species interactions that underpin species dynamics,3,4 ecosystem processes, and contributions to people.5,6,7 Yet the uniqueness of interaction networks in a regional context has rarely been assessed. Here, we estimated the spatial uniqueness of 10,000 terrestrial vertebrate trophic networks across Europe (1,164 species, 50,408 potential interactions8) based on the amount of similarity between all local networks mapped at a 10 km resolution. Our results revealed more unique networks in the Arctic bioregion, but also in southern Europe and isolated islands. We then contrasted the uniqueness of trophic networks with their vulnerability to human footprint and future climate change and measured their coverage within protected areas. This analysis revealed that unique networks situated in southern Europe were particularly exposed to human footprint and that unique networks in the Arctic might be at risk from future climate change. However, considering interaction networks at the level of trophic groups, rather than species, revealed that the general structure of trophic networks was redundant across the continent, in contrast to species' interactions. We argue that proactive European conservation strategies might gain relevance by turning their eyes toward interaction networks that are both unique and vulnerable.

Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples.

Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 µg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.

Characterization of Shiga toxin-producing Escherichia coli presence, serogroups and risk factors from private groundwater sources in western Ireland.

Over recent years, Ireland has reported the highest crude incidence rates of Shiga toxin-producing Escherichia coli (STEC) enteritis in Europe. Unregulated private groundwater sources have emerged as an important potential transmission route for STEC, with up to 750,000 Irish residents reliant on these sources for domestic waters. This study aimed to investigate the prevalence and serogroup profile of STEC contamination from domestic private wells in western Ireland. Fifty-two groundwater sources were analysed during two sampling campaigns in the autumn (September/October) of 2019 (n = 21) and 2021 (n = 31). Untreated groundwater samples (30 L) were collected and analysed using the "CapE" (capture, amplify, extract) method. Extracted DNA was tested using multiplex real-time PCR for Shiga toxin stx1 and/or stx2 and eae genes. STEC positive DNA samples were tested for clinically relevant serogroups by real-time PCR. Data relating to 27 potential groundwater contamination risk factors were geospatially linked to each well and assessed for association with E. coli, stx1 and/or stx2 and eae presence/absence. Overall, 20/52 wells (38.4 %) were positive for E. coli (median concentration 8.5 MPN/100 mL as assessed by Colilert-18 method). Stx1 and/or stx2 was detected in 10/52 (19.2 %) wells overall and 8/20 E. coli positive wells, equating to a STEC to "generic" E. coli detection ratio of 40 %. Six of these wells (30 %) were also positive for eae. One or more serogroup-specific gene targets were identified in all but one stx1 and/or stx2 positive sample, with O145 (n = 6), O157 (n = 5) and O103 (n = 4) most prevalent. STEC presence was significantly associated with decreasing well depth (U = -2.243; p = 0.024) and increasing 30-day mean antecedent rainfall (U = 2.126; p = 0.034). Serogroup O104 was associated with increased sheep density (U = 2.089; p = 0.044) and detection of stx1 and/or stx2 + eae with increased septic tank density (U = 2.246 p = 0.023). Findings indicate high detection rates of clinically relevant STEC in E. coli contaminated groundwater sources in Ireland.

Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage.

The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.

Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.

Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ2 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.